FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39056441", "kind": "science-record", "revision": 4, "content_hash": "sha256:416dc16f9d4c2f20d1fc5010772909ff177073ab3872cf78649d6d4d735240b5", "created_at": "2026-11-01T20:29:08Z", "updated_at": "2026-11-01T22:54:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei.", "doi": "10.1021/acs.jproteome.4c00161", "pmid": "39056441", "authors": ["Lucy Bedwell", "Myrto Mavrotas", "Nikita Demchenko", "Reuben M Yaa", "Brittannie Willis", "Zuzana Demianova", "Nelofer Syed", "Harry J Whitwell", "Alexi Nott"], "journal": "Journal of proteome research", "year": 2024, "abstract": "Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programs, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localized to the nucleus; however, nuclear-localized proteins are often underrepresented in gene expression studies and have been understudied in the context of the brain. To address this challenge, we have optimized an approach for nuclei isolation that is compatible with proteomic analysis. This was coupled to a mass spectrometry protocol for detecting proteins in low-concentration samples. We have generated nuclear proteomes for neurons, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclear proteins associated with chromatin structure and organization, chromatin modifiers such as transcription factors, and RNA-binding proteins, among others. Our nuclear proteomics platform paves the way for assessing brain cell type changes in the nuclear proteome across health and disease, such as neurodevelopmental, aging, neurodegenerative, and neuroinflammatory conditions. Data are available via ProteomeXchange with the identifier PXD053515.", "claims": [{"id": "claim-method", "statement": "Analysis of variance (ANOVA) and simple linear regression tests were performed using GraphPad Prism 9 (GraphPad Software, San Diego, California, USA). A posthoc multiple comparison test (Tukey) was used to determine the statistical difference between conditions for ANOVA tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39056441", "locator": "sections[12] \"Statistics\" paragraph 2", "quote": "Analysis of variance (ANOVA) and simple linear regression tests were performed using GraphPad Prism 9 (GraphPad Software, San Diego, California, USA). A posthoc multiple comparison test (Tukey) was used to determine the statistical difference between conditions for ANOVA tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability StatementThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE55 partner repository with the data set identifier PXD053515.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39056441", "locator": "sections[15] \"notes\" paragraph 1", "quote": "Data Availability StatementThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE55 partner repository with the data set identifier PXD053515."}], "state": "complete"}, {"id": "claim-target-result", "statement": "For the registered target, the paper used analysis of variance (ANOVA) and simple linear regression, with the underlying mass-spectrometry proteomics data deposited in ProteomeXchange via PRIDE under PXD053515.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39056441", "locator": "sections[12] \"Statistics\" paragraph 2", "quote": "Analysis of variance (ANOVA) and simple linear regression tests were performed using GraphPad Prism 9 (GraphPad Software, San Diego, California, USA)."}, {"asset": "source:pmid:39056441", "locator": "sections[13] \"Results\" paragraph 6", "quote": "There was a linear increase in the number of identified proteins with the number of unpelleted nuclei (Figure 2D, E, Supplemental Table 1)."}, {"asset": "source:pmid:39056441", "locator": "sections[15] \"notes\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE55 partner repository with the data set identifier PXD053515."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "For the registered target, the paper used analysis of variance (ANOVA) and simple linear regression, with the underlying mass-spectrometry proteomics data deposited in ProteomeXchange via PRIDE under PXD053515.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39056441"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD053515"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD053515"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39056441", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.jproteome.4c00161", "sha256": "sha256:c95f70adb159e0c6d0fe55edebd8c1bfe3fdb81a00ea4bd183320d94f20df813", "bytes": 37298, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.jproteome.4c00161", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11385383", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD053515", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD053515", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD053515", "version": null, "note": "Data Availability StatementThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE55 partner repository with the data set identifier PXD053515.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability StatementThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE55 partner repository with the data set identifier PXD053515.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "FANS unfixed: isolation and proteomic analysis of mouse cell type-specific brain nuclei", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD053515 not downloaded", "asset:data:geo:PXD053515 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Analysis of variance (ANOVA) and simple linear regression tests were performed using GraphPad Prism 9 (GraphPad Software, San Diego, California, USA). A posthoc multiple comparison test (Tukey) was used to determine the statistical difference between conditions for ANOVA tests."}}, {"id": "method-2", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "linear regression"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD053515"], "resolved_accessions": ["PXD053515"], "statements": ["Data Availability StatementThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE55 partner repository with the data set identifier PXD053515."], "basis": "The paper names PXD053515 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:39056441", "data:geo:PXD053515"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD053515"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:25:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10518, "completion_tokens": 1130, "cached_tokens": 0}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:39056441", "type": "paper", "label": "pmid:39056441"}, {"id": "source:pmid:39056441", "type": "manuscript", "label": "PMID 39056441 full text"}, {"id": "data:geo:PXD053515", "type": "dataset", "label": "GEO PXD053515"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39056441", "type": "paper", "label": "pmid:39056441"}, {"id": "source:pmid:39056441", "type": "manuscript", "label": "PMID 39056441 full text"}, {"id": "data:geo:PXD053515", "type": "dataset", "label": "GEO PXD053515"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39056441", "type": "extraction", "used": ["source:pmid:39056441"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD053515", "type": "accession_resolution", "used": ["data:geo:PXD053515"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39056441", "parent_hash": "sha256:bf4a724837944a7767832e45e3adf3da49382187eca5ef00dd1042a2e90a722e", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD053515 licence not read", "asset:data:geo:PXD053515 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei.", "ns, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclea", "brains from adult (∼8 weeks) female C57BL/6J mice were sourced from Charles River UK, Ltd. Unless o", "clei isolation, followed by proteomics. Bulk mouse brain proteomics (whole cell lysates) was pe"], "order_basis": "paper_text_order:5", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Analysis of variance (ANOVA) and simple linear regression tests were performed using GraphPad Prism 9 (GraphPad Software, San Diego, California, USA). A posthoc multiple comparison test (Tukey) was used to determine the statistical difference between conditions for ANOVA tests."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}